6AEM | pdb_00006aem

Crystal structure of the PKD1 domain of Vibrio anguillarum Epp

• PDB DOI: https://doi.org/10.2210/pdb6AEM/pdb

• Classification: UNKNOWN FUNCTION
• Organism(s): Vibrio anguillarum
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2018-08-05 Released: 2018-12-12 
• Deposition Author(s): Ma, Q., Li, P.
• Funding Organization(s): Chinese Academy of Sciences

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free: 
  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work: 
  0.151 (Depositor), 0.162 (DCC) 
• R-Value Observed: 
  0.153 (Depositor) 

Starting Model: experimental

Literature

Structural basis for specific calcium binding by the polycystic-kidney-disease domain of Vibrio anguillarum protease Epp

Li, P., Zang, K., Li, Y., Liu, C., Ma, Q.

(2018) Biochem Biophys Res Commun 505: 471-477

• PubMed: 30268503 
• DOI: https://doi.org/10.1016/j.bbrc.2018.09.108
• Primary Citation Related Structures: 
  6AEM


• PubMed Abstract: 
  

  Extracellular proteases are often produced as pre-pro-enzyme and then undergo multiple processing steps to mature into the active form. The protease Epp, a virulent factor of Vibrio anguillarum, belongs to this family. Its maturation might be regulated by Ca ²⁺ via its polycystic kidney disease (PKD) domain, but the molecular mechanism is unknown. Herein, we report the crystal structure of the first PKD domain from V. anguillarum Epp (Epp-PKD1) and its specific Ca ²⁺ -binding capacity. Epp-PKD1 exists as a monomer, consisting of seven β-strands which form two β-sheets stacking with each other. One Ca ²⁺ is bound by the residues Asn3, Gln4, Asp27, Asp29, Asp68 and a water molecule with a pentagonal bipyramidal geometry. Incubating the apo Epp-PKD1 with Ca ²⁺ but not Mg ²⁺ , Mn ²⁺ , or Zn ²⁺ , enhances the thermal and chemical stability of Epp-PKD1, indicating its specific binding to Ca ²⁺ . Epp-PKD1 shares high similarity in both sequence and overall structure with that of Vibrio cholerae PrtV, a homologous protease of Epp, however, they differ in the oligomeric state and local structure at the Ca ²⁺ -binding site, suggesting maturation of PrtV and Epp might be differently regulated by Ca ²⁺ . Likely, proteases may take advantage of the structural diversity in PKD domains to tune their Ca ²⁺ -regulated maturation process.

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Organizational Affiliation: 
• Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; University of Chinese Academy of Sciences, Beijing, China.
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China; Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China; Center for Ocean Mega-Science, Chinese Academy of Sciences, Qingdao, China. Electronic address: [e-mail].

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 19.29 kDa 
• Atom Count: 1,513 
• Modeled Residue Count: 168 
• Deposited Residue Count: 174 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
PKD domain	A, B	87	Vibrio anguillarum	Mutation(s): 0
UniProt
Find proteins for A0A383R4X5 (Vibrio anguillarum) Explore A0A383R4X5  Go to UniProtKB:  A0A383R4X5

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	D [auth A], E [auth A], F [auth A], H [auth B], I [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
CA (Subject of Investigation/LOI)	C [auth A], G [auth B]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.27 Å
• R-Value Free:  0.186 (Depositor), 0.194 (DCC) 
• R-Value Work:  0.151 (Depositor), 0.162 (DCC) 
• R-Value Observed: 0.153 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.096	α = 90
b = 46.069	β = 97.39
c = 41.616	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
PHASER	phasing

Structure Validation

Entry History 

& Funding Information

Deposition Data

• Released Date: 2018-12-12 
Deposition Author(s): Ma, Q., Li, P.

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Funding Organization	Location	Grant Number
	China	1000 talent program
Chinese Academy of Sciences	China	100 talent program

Revision History  

• Version 1.0: 2018-12-12
  Type: Initial release
  
• Version 1.1: 2023-11-22
  Changes: Data collection, Database references, Derived calculations, Refinement description